Chewtobacca said:

I have successfully ruled out the hard drive's being the issue. It might be the length of the clips. I have no clips of comparable length to hand and don't fancy ripping two versions of a similar length film to my hard drive to test it out. I'm about ready to give up, to be honest.

Option: Render with ColourLikeFBF in several (2? 3?) smaller pieces to an intermediate lossless format (e.g., Lagarith) and then do a second render that includes joining the pieces together.